AMBER Archive (2007)

Subject: Re: AMBER: Re: ff02 and ff03 parameters

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Jun 25 2007 - 18:28:02 CDT

this is expected, the different force fields have different numbers of terms
in the dihedral expansion for the dihedrals in your system. it might be
worth
reading the two papers in detail, especially for ff02 which is very
different than ff03
and in my opinion should be used with caution unless you really know what
you are doing.

On 6/25/07, Pavan G <pavanamber_at_gmail.com> wrote:
>
> Hello all,
>
> >
> > Recently I used amber8's ff02 and amber9's ff03 forcefields to generate
> > parameters for a protein I am working on and I ended up with two different
> > prmtop files. I would expect the output to be the same but here are the
> > differences
> >
> > ff02 ff03
> > 1960 1960 NATOM : total number of atoms
> > 14 14 NTYPES : total number of distinct atom types
> > 959 959 NBONH : number of bonds containing hydrogen
> > 1025 1025 MBONA : number of bonds not containing hydrogen
> > 2158 2158 NTHETH : number of angles containing hydrogen
> > 1389 1389 MTHETA : number of angles not containing hydrogen
> > 4149 4245 NPHIH : number of dihedrals containing
> > hydrogen <-------------------- different
> > 2555 2928 MPHIA : number of dihedrals not containing
> > hydrogen <-------------------- different
> > 0 0 NHPARM : currently not used
> > 0 0 NPARM : currently not used
> > 10733 10733 NEXT : number of excluded atoms
> > 129 129 NRES : number of residues
> > 1025 1025 NBONA : MBONA + number of constraint bonds
> > 1389 1389 NTHETA : MTHETA + number of constraint angles
> > 2555 2928 NPHIA : MPHIA + number of constraint
> > dihedrals <-------------------- different
> > 39 41 NUMBND : number of unique bond
> > types <-------------------- different
> > 84 90 NUMANG : number of unique angle
> > types <-------------------- different
> > 40 48 NPTRA : number of unique dihedral
> > types <-------------------- different
> > 26 27 NATYP : number of atom types in parameter file, see
> > SOLTY below <-------------------- different
> > 0 0 NPHB : number of distinct 10-12 hydrogen bond pair
> > types
> >
> >
> > The pdb file (without hydrogens) and the two prmtop files are at:
>
>
> http://compbio.ornl.gov/~pkc/ff02.prmtop>
> http://compbio.ornl.gov/~pkc/ff03.prmtop>
> http://compbio.ornl.gov/~pkc/pro-noh.pdb
> <http://compbio.ornl.gov/%7Epkc/pro-noh.pdb>
>
> Could someone explain me why the same protein should have different
> > parameters. Specifically,
> > why should the total number of dihedrals shoot up by 439 on changing the
> > forcefield.
> >
> > Thanks.
> >
> >
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
Center for Structural Biology       Fax:   (631) 632-1555
CMM Bldg, Room G80
Stony Brook University              E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115          Web: http://comp.chem.sunysb.edu
===================================================================

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